[BioC] How to convert Illumina ProbeIDs to nuIDs without nuID indexed annotation libraries?

[Pan Du]

Hi Elliot,

You can find the Illumina ID mapping packages, lumiHumanIDMapping.db and
lumiMouseIDMapping.db, in the Bioc 2.3 (Developing). These packages include
all types of Illumina IDs and corresponding nuIDs. To do ID mapping, you
also need to update the lumi package to the developing version lumi 1.7.23.
Please read the vignette "IlluminaAnnotation.pdf" before using them. All
these packages can be installed and ran in R 2.7 or above. If you are using
R 2.7, you need to manually download and install them,  biocLite cannot
install developing version packages.
Tell me if you have any questions.


Pan



On 9/23/08 5:00 AM, "bioconductor-request at stat.math.ethz.ch"
<bioconductor-request at stat.math.ethz.ch> wrote:

> Message: 3
> Date: Tue, 23 Sep 2008 00:39:50 -0700
> From: Elliot Kleiman <kleiman at rohan.sdsu.edu>
> Subject: [BioC] How to convert Illumina ProbeIDs to nuIDs without nuID
> indexed annotation libraries?
> To: bioconductor at stat.math.ethz.ch
> Message-ID: <48D89D46.2050405 at rohan.sdsu.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> Hi BioC,
> 
> [Question]:
> * How do you convert Illumina ProbeIDs to nuIDs without nuID
> indexed annotation libraries?
> 
> i.e.,
> 
> ... the following previous BioC 2.1 released nuID indexed annotation
> libraries,
> 
> * lumiRatV1
> * lumiMouseV1
> * lumiHumanV1
> * lumiHumanV2
> 
> ... are not available in BioC release 2.2,
> * http://www.bioconductor.org/packages/2.2/data/annotation/
> 
> RE: My objective is to map probeIDs to nuIDs standalone without
> first having to create a lumiBatch object via the lumi package.
> 
> There is a new annotation package, 'lumiRatAll.db' in BioC 2.2,
> but it doesn't provide the functional mapping of ProbeIDs to nuIDs;
> it assumes you already have nuIDs.
> 
> e.g.,
> The lumi package offers a function that can map Illumina probeIDs
> to nuIDs, 'probeID2nuID()'. But the problem is that it requires
> a 'lib' argument to specify a nuID indexed annotation library
> (none of which are currently available in the current 2.2 release).
> * http://www.bioconductor.org/packages/2.2/data/annotation/
> 
> e.g.,
> 
> # load lumi package from BioC release 2.2
>> library(lumi)
> 
> # get help on lumi function probeID2nuID
>> help(probeID2nuID)
> 
> Print-out excerpt of help documentation for function
> 'probeID2nuID()' from package 'lumi',
> 
> # probeID2nuID              package:lumi              R Documentation
> # Usage:
> # probeID2nuID(probeID, lib = "lumiHumanV1")
> # Arguments:
> # probeID: a vector of Illumina ProbeID
> # lib: a nuID indexed Illumina annotation library
> 
> e.g.
> # Not Run b/c no annotation libs loaded b/c they aren't available to install
>> nu <- probeID2nuID(pid, lib = "lumiHumanV1")
> 
> Am I [like totally] missing something here?
> 
> Thanks,
> 
> ... Elliot
> 
>> # print sessionInfo()
>> sessionInfo()
> R version 2.7.2 (2008-08-25)
> i686-pc-linux-gnu
> 
> locale:
> LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=C;LC_MONETARY=C;LC_MESSAG
> ES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=e
> n_US;LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] splines   tools     stats     graphics  grDevices utils     datasets
> [8] methods   base
> 
> other attached packages:
>  [1] illuminaRatv1ProbeID.db_1.1.1 GOstats_2.6.0
>  [3] Category_2.6.0                genefilter_1.20.0
>  [5] survival_2.34-1               RBGL_1.16.0
>  [7] GO.db_2.2.0                   graph_1.18.1
>  [9] lumiRatAll.db_1.2.0           lumi_1.6.2
> [11] mgcv_1.4-1                    beadarray_1.8.0
> [13] affy_1.18.2                   preprocessCore_1.2.1
> [15] affyio_1.8.1                  geneplotter_1.18.0
> [17] annotate_1.18.0               xtable_1.5-3
> [19] AnnotationDbi_1.2.2           RSQLite_0.7-0
> [21] DBI_0.2-4                     lattice_0.17-14
> [23] Biobase_2.0.1                 limma_2.14.6
> 
> loaded via a namespace (and not attached):
> [1] KernSmooth_2.22-22 RColorBrewer_1.0-2 cluster_1.11.11
> grid_2.7.2       
> [5] tcltk_2.7.2
> 
> -- 
> __________________________
> MS graduate student
> Program in Computational Science
> San Diego State University
> http://www.csrc.sdsu.edu/
> http://www.rohan.sdsu.edu/~kleiman/
>